scholarly journals Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0258019
Author(s):  
Ishtiaque Ahammad ◽  
Mohammad Uzzal Hossain ◽  
Anisur Rahman ◽  
Zeshan Mahmud Chowdhury ◽  
Arittra Bhattacharjee ◽  
...  
Keyword(s):  
Average Rate ◽  
Spike Protein ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Dynamic Nature ◽  
Genomic Study ◽  
The World ◽  
Comparative Genomic Study ◽  
Second Wave ◽  
Successful Prevention

As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.

scholarly journals Draft Genome Sequences of Pantoea agglomerans Strains BD1274 and BD1212, Isolated from Onion Seeds, Reveal Major Differences in Pathogenicity and Functional Genes

2020 ◽  
Vol 9 (45) ◽  
Author(s):  
Valery M. Moloto ◽  
Teresa Goszczynska ◽  
Ahmed Idris Hassen ◽  
Rian Pierneef ◽  
Teresa Coutinho
Keyword(s):  
Allium Cepa ◽  
Draft Genome ◽  
Pantoea Agglomerans ◽  
Disease Symptom ◽  
Functional Genes ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Content Type ◽  
Genomic Study ◽  
Comparative Genomic Study

ABSTRACT Pantoea agglomerans strains BD1274 and BD1212 were isolated from Allium cepa seeds. Strain BD1274 induced a disease symptom on a healthy onion, whereas strain BD1212 did not and remains nonpathogenic. A comparative genomic study revealed that the strains differ in their genomic compositions, particularly in the genes that confer pathogenicity.

scholarly journals Complete Genome Sequence of Streptococcus mutans Strain MD, Which Produces Highly Potent Mutacins

2020 ◽  
Vol 9 (33) ◽  
Author(s):  
Saswati Biswas ◽  
Indranil Biswas
Keyword(s):  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Comparative Genomic ◽  
Content Type ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Genome Information

ABSTRACT Here, we report the complete genome sequence of Streptococcus mutans strain MD, which produces potent mutacins capable of inhibiting streptococci. MD is a relatively uncharacterized strain whose genome information was unavailable. This study provides useful information for comparative genomic study and for understanding the repertoire of mutacins in S. mutans.

scholarly journals PanFunPro: PAN-genome analysis based on FUNctional PROfiles

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 265 ◽  
Author(s):  
Oksana Lukjancenko ◽  
Martin Christen Thomsen ◽  
Mette Voldby Larsen ◽  
David Wayne Ussery
Keyword(s):  
Genome Analysis ◽  
Markov Models ◽  
Epidemiological Studies ◽  
Comparative Genomic ◽  
Functional Domain ◽  
Homologous Proteins ◽  
Pan Genome ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Functional Profiles

PanFunPro is a tool for pan-genome analysis that integrates functional domains from three Hidden Markov Models (HMM) collections, and uses this information to group homologous proteins into families based on functional domain content. We use PanFunPro to compare a set of Lactobacillus and Streptococcus genomes. The example demonstrates that this method can provide analysis of differences and similarities in protein content within user-defined sets of genomes. PanFunPro can find various applications in a comparative genomic study, starting with the basic comparison of newly sequenced isolates to already existing strains, and an estimation of shared and specific genomic content. Furthermore, it can potentially be used in the determination of target sequences for in silico bacterial identification, as well as for epidemiological studies.

scholarly journals Stable Positions of Epigenetically Inherited Centromeres in the Emerging Fungal Pathogen Candida auris and Its Relatives

mBio ◽  
2021 ◽  
Author(s):  
Laura N. Rusche
Keyword(s):  
Fungal Pathogen ◽  
Evolutionary History ◽  
Comparative Genomic ◽  
Candida Auris ◽  
Content Type ◽  
Genomic Study ◽  
Comparative Genomic Study

Candida auris is an emerging fungal pathogen that is thermotolerant and often resistant to standard antifungal treatments. To trace its evolutionary history, the Sanyal lab conducted a comparative genomic study focusing on the positions of centromeres in C. auris and eight other species from the Clavispora / Candida clade of yeasts (A.

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals The emergence of SARS-CoV-2 by an unusual genome reconstitution

2020 ◽  
Author(s):  
Seong-Tshool Hong ◽  
Md. Mehedi Hassan ◽  
Shirina Sharmin ◽  
Jinny Hong ◽  
Hoi-Seon Lee ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Pairwise Comparison ◽  
Surface Protein ◽  
Plasmodium Malariae ◽  
Spike Protein ◽  
Genome Sequences ◽  
The World ◽  
The Common ◽  
Virus Strains

Abstract SARS-CoV-2 has been spreading remarkedly fast around the world since its emergence while the origin of the virus remains ambiguous. Here, we constructed all of the original prototype genome sequences of SARS-CoV-2 by selecting the common nucleotide among the different virus strains with species. Phylogenetic analysis on the prototype sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pan-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of 7 amino acids within the spike protein of SARS-CoV-2. Database searches showed that the motif originated from a surface protein of Plasmodium malariae, suggesting that the SARS-CoV-2 was emerged after acquiring the motif of the malaria surface protein.

scholarly journals Association of Sequence types, Antimicrobial Resistance and Virulence Genes in India isolates of Klebsiella pneumoniae: A Comparative Genomics Study

2021 ◽  
Author(s):  
Abhirami Krishnamoorthy Sundaresan ◽  
Keerthana Vincent ◽  
Ganesh Babu Malli Mohan ◽  
Jayapradha Ramakrishnan
Keyword(s):  
Comparative Genomics ◽  
Klebsiella Pneumoniae ◽  
Virulence Genes ◽  
Respiratory Infections ◽  
Comparative Genomic ◽  
Clinical Strains ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Phylogenetic Evolution ◽  
Tract Infections

Abstract Klebsiella pneumoniae is an important ESKAPE pathogen that causes sepsis, urinary tract infections, peritonitis, intraabdominal abscesses and upper respiratory infections. The strains exhibiting multidrug resistance and hypervirulence are priority pathogens for which immediate treatment and dissemination prevention strategies are required. The hypervirulent drug resistant K. pneumoniae is associated with high mortality rates. Numbers of environmental strains also have acquired virulence genes. Hence to gain a better understanding of the spread of antimicrobial resistant genes across the country over 10 years and to delineate environmental and clinical K. pneumoniae, a comparative genomics investigation was made. This is the first comparative genomic study using India isolates of K. pneumoniae, which includes publicly available WGS of 144 clinical and 9 environmental strains collected during 2010–2020. The blaCTX-M-15 was widely distributed in clinical isolates since 2013 and increased over time from 5 % to 30 %. The co-existence of blaNDM and blaOXA was observed in 22 % of clinical strains. Diverse serotypes were found among the 153 K. pneumoniae isolates, of which, K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). And more than 50% of KL51 strains were found to have both rmpA and magA. The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, alls,) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. Of greatest concern, these virulence genes are observed in environmental strains aswell. More than 97% of clinical strains have yersinibactin (ybtS), aerobactin (iutA) genes. Importantly, 98% of ESBL and 62% of carbapenamasen isolates harboured ybtS, iutA and rmpA, magA respectively. The IncF conjugative plasmids are predominant in K. pneumoniae, which contribute to the spread of AMR, and virulence genes. The increasing trend in hypervirulent strains was observed from 2017. The phylogenetic analysis separates the environmental from clinical strains and is characterized by uncommon STs and serotypes. Thus, the study illustrates the K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.

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